Dr. Michael Ruscio, DC is a clinician, Naturopathic Practitioner, clinical researcher, author, and adjunct professor at the University of Bridgeport. His work has been published in peer-reviewed medical journals and he speaks at conferences around the globe.
While there are 1000s of probiotic species, almost all of them can be classified into three categories.
You don’t need to match specific probiotic species to your health conditions.
For maximum benefit, take all three categories of probiotics together.
Your gut is home to a thriving community of good bacteria that work together to keep you healthy. Probiotics are live microorganisms, often consumed in fermented foods or as dietary supplements to support your native bacteria. The use of probiotics is widely known to support health, but there is a lot of conflicting advice about how to use them.
If you’re confused by what’s the best probiotic, you’re not alone. Let me simplify this for you, and help you understand how to easily select the best probiotics.
Only 3 Main Types of Probiotics
While there are 1000s of specific probiotic species, there are really only three different types of probiotics.
If you look at research on probiotics, one study might show that a combination of Lactobacillus acidophilus and Lactobacillus casei reduces IBS symptoms and another study might show that Saccharomyces boulardii helps IBS. So which one is right?
The answer is, they both are.
Each category of probiotic seems to occupy an important niche in your gut ecology and multiple species of beneficial bacteria collectively provide the health benefits of probiotics.
One single probiotic species is unlikely to be the magic pill that solves all health problems. But multiple species taken together are able to outcompete against bad bacteria and keep your gut environment healthy.
Let’s take a look at what we know about each probiotic category.
Category 1: Lactobacillus
and Bifidobacterium Probiotic Blends
This category of probiotics is the most well-researched, with over 500 clinical trials. These live microorganisms are also known as lactic-acid producing probiotic bacteria. They typically do not colonize you, but do improve your health.
This category of probiotics usually contains a blend of various Lactobacillus species and Bifidobacterium species.
Most Lactobacilli species are transient but important; There are over a hundred species.
Bifidobacterium typically reside in the large intestine; There are over thirty species.
Examples of Type 1 Probiotic Strains
Lactobacillus acidophilus Lactobacillus casei Lactobacillus gasseri Lactobacillus GG Lactobacillus reuteri Lactobacillus rhamnosus Lactobacillus plantarum
Reduce bacterial overgrowths, gas production, and abdominal pain in the small intestine. 
Though many promote Lactobacillusprobiotics for weight loss, several meta-analyses have only shown modest improvements in weight loss.
Category 2: Saccharomyces
This is the second most researched probiotic, with over 100 studies. Saccharomyces boulardii (S. boulardii for short) is a beneficial yeast that is not a normal part of the human gut microbiota. It does not colonize your gut. S. boulardii has been used successfully in research for:
The third most researched category of probiotics is soil-based probiotics. This category of probiotic can colonize your gut . These live microorganisms are also known as spore-forming or soil-based bacteria. This is because they are found everywhere in soil and water, and they often spend part of their life cycle in a dormant “spore” state.
Soil-based probiotics may help replace missing bacteria due to our reduced contact with soil and natural environments.
A number of soil-based species  show health benefits including Bacillus coagulans and Bacillus subtilis.
Research shows the following health benefits for soil-based probiotics:
Secrete antimicrobial peptides, meaning they are actually antimicrobial
Some Bacillus bacteria are harmful, so use a product that is well-labeled and independently lab tested. These types of probiotics should be avoided in critically ill patients, but otherwise are very safe. 
Benefits of Probiotics
As you can see, each of the three types of probiotics have many health benefits for gut flora and can help with many health concerns. Thankfully, to experience the benefits of probiotics, you don’t need to match specific probiotic species to your health conditions. The biggest benefit of probiotics is that they work generally. By applying a simple, general approach, probiotics provide the health benefits your body needs, and generally don’t cause side effects.
How to Use Probiotic Supplements
To get the maximum benefit from your probiotic products, choose one high-quality probiotic from each category and use them together.
Multiple probiotics work together synergistically to improve the health of your digestive system. Research suggests that using multiple strains or species of probiotics is more effective than using one single strain or species. [41, 42]
This mirrors my experience with patients in the clinic. Many patients don’t seem to achieve balance with one probiotic formula alone. Like the legs of a three-legged stool, the three probiotic protocol promotes digestive system balance. For many patients who have tried probiotics unsuccessfully in the past, this approach finally delivers results.
Probiotics aren’t closely regulated by the FDA, so you need to do your own homework to make sure you’re getting quality products. Here are some tips for choosing quality probiotics.
What to Look for in a Probiotic Supplement
A clearly stated list of species
A clearly stated number of colony-forming units (CFUs) in the billions
A manufacture date and/or expiration date
Labeled free of common allergens and other substances you may wish to avoid (e.g. gluten-free, non-GMO, vegan)
Good Manufacturing Practices (GMP) certification
Lab-verified for probiotic species and potency by third-party analysis (independent lab testing)
Fermented foods are cultured with beneficial bacteria, such as Lactobacillus bulgaricus and Streptococcus thermophilus and can be a tasty part of your health strategy. But probiotic foods, like sauerkraut, kimchi, kefir, miso, and kombucha, don’t contain enough probiotic colony-forming units to provide a clinical effect. If you’re trying to address a health problem with probiotics, it’s best to use a supplement protocol with higher doses of active bacteria.
Prebiotics are fermentable starches that feed your probiotics, and are often recommended alongside probiotics. Prebiotics can be either consumed as dietary supplements, or by eating a diet rich in fiber. Common food sources of prebiotic fiber include fruits and vegetables, whole grains and legumes, and nuts and seeds. You can include prebiotics to support your probiotics, but do so with caution, as they can flare some digestive health conditions.
The Bottom Line
There are really only three types of probiotics, and using all three together will likely provide the best health benefits, for your gut and your overall health. Choose one high-quality probiotic product from each category and use them together.
American College of Gastroenterology Task Force on Irritable Bowel Syndrome, Brandt LJ, Chey WD, et al. An evidence-based position statement on the management of irritable bowel syndrome. Am J Gastroenterol. 2009;104 Suppl 1:S1-S35. doi:10.1038/ajg.2008.122
Ford AC, Quigley EM, Lacy BE, et al. Efficacy of prebiotics, probiotics, and synbiotics in irritable bowel syndrome and chronic idiopathic constipation: systematic review and meta-analysis. Am J Gastroenterol. 2014;109(10):1547-1562. doi:10.1038/ajg.2014.202
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